Kramer was an early advocate of attacking Saddam Hussein in the wake of 9/11, arguing in December 2001 that regardless of a possible involvement, he posed a threat to the entire Middle East.[4] However, he was critical of the shifting rationale for the war in October 2002, questioning the United States' "tools of social engineering" needed to promote an eventual democracy process in the Arab world.[5]

He was a senior policy adviser on the Middle East to the Rudy Giuliani Presidential Campaign in 2007.[6]

In 2001, the Washington Institute for Near East Policy published Kramer's book Ivory Towers on Sand: The Failure of Middle Eastern Studies in America (download). In the book (as reported by the New York Times), Kramer argued that Middle East experts "failed to ask the right questions at the right time about Islam. They underestimated its impact in the 1980's; they misrepresented its role in the early 1990's; and they glossed over its growing potential for terrorism against America in the late 1990's." His critics claimed that “there is an agenda here, which is to discredit the entire Middle East establishment.”.[7]

At the February 2010 Herzliya Conference in Israel, Kramer caused controversy in a speech in which he advocated cuts in what he termed "pro-natal subsidies" to Palestinians in Gaza as a means of discouraging population growth, thus curbing Islamic radicalization.[8][9] At the time, he was a National Security Studies Program Visiting Scholar at the Weatherhead Center for International Affairs, Harvard University, and some critics called on Harvard to distance itself from him. Deans at Harvard University's Weatherhead Center for International Affairs rejected these calls, stating, "Accusations have been made that Martin Kramer's statements are genocidal. These accusations are baseless." They found that Kramer's critics "appear not to understand the role of controversy in an academic setting" and rejected any attempts to restrict "fundamental academic freedom."[10]